AlzCode: a Platform for Multiview Analysis of Genes Related to Alzheimer's Disease

Bioinformatics. 2022 Jan 18;btac033. doi: 10.1093/bioinformatics/btac033. Online ahead of print.

Abstract

Motivation: Alzheimer's disease (AD) is a complex brain disorder with risk genes incompletely identified. The candidate genes are dominantly obtained by computational approaches. In order to obtain biological insights of candidate genes or screen genes for experimental testing, it is essential to assess their relevance to AD. A platform that integrates different types of omics data and approaches would facilitate the analysis of candidate genes and is in great need.

Results: We report AlzCode, a platform for multiview analysis of genes related to AD. First, this platform integrates a rich collection of functional genomic data, including expression data of AD samples (gene expression, single-cell RNA-seq data, and protein expression), AD-specific biological networks (co-expression networks and functional gene networks), neuropathological and clinical traits (CERAD score, Braak staging score, Clinical Dementia Rating, cognitive function, and clinical severity), as well as general data such as protein-protein interaction, regulatory networks, sequence similarity and miRNA-target interactions. These data provide basis for analyzing genes from different views. Second, the platform integrates multiple approaches designed for the various types of data. We implement functions to analyze both individual genes and gene sets. We also compare AlzCode with two existing platforms for AD analysis, which are Agora and AD Altas. We pinpoint the features of each platform and highlight their differences. This platform would be valuable to the understanding of AD genetics and pathological mechanisms.

Availability and implementation: AlzCode is freely available at: http://www.alzcode.xyz.

Supplementary information: Supplementary data is available at Bioinformatics online.